NextPolish: a fast and efficient genome polishing tool for long-read assembly
By Jiang Hu, Junpeng Fan, Zongyi Sun, Shanlin Liu. Bioinform., 2019
1,029 citations recorded by the source corpus.
MOTIVATION While long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors. RESULTS When evaluated for the speed and efficiency using human and a plant (Arabidopsis thalina) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy. AVAILABILITY NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/24c676f9011cf20b9ca590ffd5c55844612252d4
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In Genetics
In Molecular Biology
- Aleksey V. Zimin
- Steven L. Salzberg
- Zongyi Sun
- Jiang Hu
- Heng Li
- Florian P. Breitwieser
- Nitesh V. Chawla
- Jennifer Lu
Citations in the corpus
- NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, methodology): “NextDenovo employs the Kmer score chain (KSC) algorithm which was used by our previously published polisher tool, NextPolish [19], to perform the initial rough correction (Fig.”
- The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies (2019, result): “We also compare POLCA to two newer tools, ntEdit [6] and NextPolish [7].”